Last modified by adavison on 2022/10/04 13:53
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edited by adavison
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edited by shailesh
on 2021/10/12 16:19
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1 -XWiki.adavison
1 +XWiki.shailesh
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1 -(% class="box successmessage" %)
2 -(((
3 -Video: [[https:~~/~~/www.youtube.com/watch?v=BZB7xKUK8Vc>>https://www.youtube.com/watch?v=BZB7xKUK8Vc]]
4 -)))
5 -
6 6  == Learning objectives ==
7 7  
8 -In this tutorial, you will learn how to install PyNN, together with the Brian 2, NEST and NEURON simulators, on Linux.
3 +In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux.
9 9  
10 10  (% class="box infomessage" %)
11 11  (((
12 -Note: We are preparing tutorials for Windows and Mac OS
7 +Note: There will be a separate tutorial for each environment.
13 13  )))
14 14  
15 15  == Audience ==
16 16  
17 -This tutorial is intended for people with at least a basic knowledge of neuroscience (high-school level or above) and basic familiarity with the Python programming language. It should also be helpful for people who already have advanced knowledge of neuroscience and neural simulation, who simply wish to learn how to use PyNN and how it differs from other simulation tools they know.
12 +This tutorial is intended for people with at least a basic knowledge of neuroscience (high school level or above) and basic familiarity with the Python programming language. It should also be helpful for people who already have advanced knowledge of neuroscience and neural simulation, who simply wish to learn how to use PyNN, and how it differs from other simulation tools they know.
18 18  
19 19  == Prerequisites ==
20 20  
... ... @@ -42,7 +42,7 @@
42 42  **Slide** listing learning objectives
43 43  )))
44 44  
45 -In this tutorial, I will guide you through setting up PyNN, together with the Brian 2, NEST, and NEURON simulators, on a Linux  environment. Note that we have a dedicated version of this tutorial for other environments, such as Mac OS, Windows, and EBRAINS Jupyter Lab.
40 +In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON and Brian 2 simulators, on a Linux  environment. Note that we have a dedicated version of this tutorial for other environments, such as Mac OS, Windows and EBRAINS Jupyter Lab.
46 46  
47 47  (% class="box successmessage" %)
48 48  (((
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49 49  **Slide** listing prerequisites
50 50  )))
51 51  
52 -I will demonstrate the installation on a computer with Ubuntu 20.04 OS installed. The steps are likely to remain very similar for other versions of Ubuntu OS and are also not expected to vary significantly for other Linux distributions. In the latter case, you can find information on the Internet about how to carry out the equivalent of the tasks demonstrated here. Also, this tutorial focuses only on Python 3, because Python 2 is no longer supported. It is recommended to use Python version 3.6 or higher. I will be using Python 3.8.10 in this tutorial, because it is the default version provided with Ubuntu 20.04.
47 +I shall be demonstrating the installation on a computer with Ubuntu 20.04 OS installed. The steps are likely to remain very similar for other versions of Ubuntu OS, and also not expected to vary significantly for other Linux distributions. In the latter case, you will find on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, the tutorial will focus only on Python 3, as Python 2 has now been deprecated. It is recommended to use Python version 3.6 or higher. I would be using Python 3.8.10 in this tutorial, as it is the default version provided with Ubuntu 20.04.
53 53  
54 54  (% class="box errormessage" %)
55 55  (((
56 -**Note**
57 -Having multiple versions of Python on your system can produce issues while installing NEST. The method shown below will install NEST for the default version of Python provided by your Ubuntu OS. For example, for Ubuntu 18.04, this might be Python 3.6.9, and for Ubuntu 20.04, it will likely be 3.8.10. If you wish to associate the NEST installation with a different Python version installed on your system, please refer to the NEST installation instructions to do so on their website.
51 +**Note:**
52 +Having multiple versions of Python on your system can produce issues while installing NEST. The method shown below will install NEST for the default version of Python provided by your Ubuntu OS. E.g. for Ubuntu 18.04 this might be Python 3.6.9 and for Ubuntu 20.04 it will likely be 3.8.10. If you wish to associate the NEST installation with a different Python version installed on your system, please refer the NEST installation instructions to do so on their website.
58 58  )))
59 59  
60 60  (% class="box infomessage" %)
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62 62  **Screencast** - terminal
63 63  )))
64 64  
65 -In this tutorial, we will make use of virtual environments. This allows multiple Python projects to coexist on the same computer, even when they might have different, and even conflicting, requirements. It helps isolate projects, thereby preventing unrequested changes in others, when any one of them is updated.
60 +We shall make use of virtual environments in this tutorial. This allows multiple Python projects to coexist on the same computer, even when they might have different, and even conflicting, requirements. It helps isolate projects and thereby preventing unrequested changes in others, when any one of them is updated.
66 66  
67 -Let's begin by creating a directory for our project.
62 +We begin by creating a directory for our project.
68 68  
69 69  (% class="box infomessage" %)
70 70  (((
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74 74  cd pynn_project
75 75  )))
76 76  
77 -Next, we will create a virtual environment within this directory. Python 3 provides support for creating virtual environments. To use this, we first install the package named 'python3-venv':
72 +Next we shall create a virtual environment within this directory. Python 3 provides support for creating virtual environments. Since Python 3.6, the recommended method of creating a new virtual environment is as follows:
78 78  
79 -(% class="box infomessage" %)
74 +(% class="box errormessage" %)
80 80  (((
81 -**Screencast** - terminal
82 -
83 -(% style="color:#000000" %)
84 -sudo apt-get install python3-venv
76 +**Note:**
77 +For older versions of Python 3, you might require to manually install `python3-venv` package before being able to run the below command. To install, run:
78 +\\sudo apt-get install python3-venv
79 +\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
85 85  )))
86 86  
87 -And once this is installed, we can create a new virtual environment by typing 'python3', '-m venv' to indicate the name module of the module we just installed, followed by the name we wish to assign to our virtual environment. Here, we have set this to 'pynn_env'.
88 -
89 89  (% class="box infomessage" %)
90 90  (((
91 91  **Screencast** - terminal
92 -
93 -(% style="color:#000000" %)
94 -python3 -m venv pynn_env
85 +\\(% style="color:#000000" %)python3 -m venv pynn_env
95 95  )))
96 96  
97 97  (% class="box warningmessage" %)
98 98  (((
99 -**Note**
100 -
101 -
102 -Note that this command is 'python3' and not simply 'python'. This is because Ubuntu 20, by default, understands only the former. You can find on the Internet various ways to have 'python' also refer to 'python3', but for the purposes of this tutorial, we keep things simple and try to work with the bare minimum changes to the system.
90 +**Note:**
91 +\\Observe that this command is as 'python3' and not simply 'python'. This is because Ubuntu 20, as default, understands only the former. You can find on the Internet various ways to have 'python' also refer to 'python3', but for the purposes of this tutorial we shall keep things simple and try to work with the bare minimum changes to the system.
103 103  )))
104 104  
105 -This will create a sub-directory named 'pynn_env' within our project directory, with several files and sub-directories. Let's take a look at the 'site-packages' directory.
94 +This will create a sub-directory named 'pynn_env' within our project directory, with several files and sub-directories. Let us take a look at the 'site-packages' directory.
106 106  
107 107  (% class="box infomessage" %)
108 108  (((
109 109  **Screencast** - file explorer
110 -\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
99 +\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.9/site-packages >>
111 111  )))
112 112  
113 -As you see here, only a limited number of basic packages have currently been installed in this virtual environment. In the steps ahead, we will install various other packages, which you will be able to see here.
102 +As you see here, only a limited number of basic packages have currently been installed in this virtual environment. In the steps ahead, we shall install various other packages, and you shall see that these would be reflected here.
114 114  
115 -To enter this virtual environment, and thereby use its resources in isolation from other projects on your computer, we have to "activate" it. This is achieved by running the command:
104 +To enter into this virtual environment, and thereby use its resources in isolation from other projects on your computer, we require to "activate" it. This is achieved by running the command:
116 116  
117 117  (% class="box infomessage" %)
118 118  (((
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120 120  \\(% style="color:#000000" %)source pynn_env/bin/activate
121 121  )))
122 122  
123 -Notice how this changes the command prompt to show the name of your virtual environment. In our case, we have named it 'pynn_env', and this is now reflected as a prefix to the command prompt. This confirms that we are now in our new virtual environment.
112 +Notice how this changes the command prompt to show the name of your virtual environment. In our case, we had named it 'pynn_env', and this is now reflected as a prefix to the command prompt. This confirms that we are now in our new virtual environment.
124 124  
125 125  (% class="box warningmessage" %)
126 126  (((
127 -**Note**
128 -
129 -
130 -You might be required to run the above command every time you open a new terminal window. Check that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
116 +**Note:**
117 +\\You might be required to run the above command every time you open a new terminal window. Do verify that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
131 131  )))
132 132  
133 -Before we proceed, let us run the following commands to ensure that our environment is setup as required:
120 +Now that we have our project's virtual environment setup, we are now ready to install PyNN and other simulators. In general, it is advisable to install the various simulators (especially NEURON and NEST) prior to installing PyNN, because PyNN will then auto compile NEURON's NMODL fles and NEST's extensions during installation. In this tutorial, we will adopt this approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
134 134  
135 -
136 -(% class="box infomessage" %)
137 -(((
138 -**Screencast** - terminal
139 -\\(% style="color:#000000" %)pip install ~-~-upgrade pip
140 -sudo apt install make
141 -)))
142 -
143 -Now that we have our project's virtual environment setup, we are ready to install PyNN and other simulators. In general, it is advisable to install the various simulators (especially NEURON and NEST) prior to installing PyNN, because PyNN will then auto compile NEURON's NMODL fles and NEST's extensions during installation. In this tutorial, we will adopt this approach and begin by installing the simulators. For the purposes of this tutorial, we will demonstrate the installation of Brian2, NEST, and NEURON simulators.
144 -
145 145  (% class="box errormessage" %)
146 146  (((
147 147  **Note:**
148 -\\If you have previously installed NEURON or NEST on your system and are installing PyNN now, you will have to compile NEURON's NMODL fles and NEST's extensions manually. For more instructions on this, take a look at:
125 +\\If you have previously already installed NEURON or NEST on your system and are installing PyNN now, then you would require to compile NEURON's NMODL fles and NEST's extensions manually. For more instructions on this, take a look at:
149 149  [[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
150 150  )))
151 151  
152 -We start here with the installation of Brian 2. Brian 2 can be installed simply by using the pip command.
129 +We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
153 153  
154 154  (% class="box infomessage" %)
155 155  (((
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157 157  \\(% style="color:#000000" %)pip install brian2
158 158  )))
159 159  
160 -This will install Brian 2, along with all its dependencies such as 'cython', 'numpy', and so on. We can now go back to our virtual environment's 'site-packages' directory to see how it is populated with all these packages.
137 +This will install Brian 2, along with all its dependencies such as 'cython', 'numpy', etc. We can now go back into our virtual environment's 'site-packages' directory to see how it is now populated with all these packages.
161 161  
162 162  (% class="box infomessage" %)
163 163  (((
164 164  **Screencast** - file explorer
165 -\\(% style="color:#000000" %)<< show directory contents lib/python3.8/site-packages >>
142 +\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
166 166  )))
167 167  
168 168  To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
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177 177  
178 178  (% class="box warningmessage" %)
179 179  (((
180 -**Note**
181 -\\You might remember that, earlier in this tutorial, we had to use the term 'python3' to run Python on our system. But here, as in the rest of this tutorial, we will simply write 'python'. This is possible because, once we have activated our virtual environment, this environment understands that both 'python' and 'python3' are equivalent.
157 +**Note: **
158 +\\You might remember that earlier in this tutorial we had to use the term 'python3' to run Python on our system. But here, as in the rest of this tutorial, we shall simply write 'python'. This is possible because once we have activated our virtual environment, this environment understands that both 'python' and 'python3' are equivalent.
182 182  )))
183 183  
184 -If there are no error messages here, and the import is successful, we have completed the installation of Brian 2.
161 +If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
185 185  
186 -We will now move on to install the NEST simulator. Unlike Brian 2, NEST is not a Python package and therefore, it cannot be installed via the 'pip' command.
163 +We shall now move on to install the NEST simulator. Unlike Brian 2, NEST is not a Python package and therefore it cannot be installed via the 'pip' command.
187 187  
188 -At the time of creating this tutorial, the latest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST are potentially incompatible with this version of PyNN. The installation is done by first adding the PPA repository for NEST and updating apt, followed by the installation of NEST itself.
165 +At the time of creating this tutorial, the lastest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST could potentially be incompatible with this version of PyNN. The installation is done by first adding the PPA repository for NEST and updating apt, followed by the installation of NEST itself.
189 189  
190 190  (% class="box infomessage" %)
191 191  (((
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201 201  (((
202 202  **Screencast** - terminal
203 203  \\(% style="color:#000000" %)nest
204 -
205 -(% style="color:#000000" %)exit
206 206  )))
207 207  
208 -This will display the NEST banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEST v3.1 on our system. Next, let's verify that this is indeed accessible via Python.
183 +This will display the NEST banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEST v3.1 on our system. Let us next verify that this is indeed accessible via Python.
209 209  
210 210  (% class="box infomessage" %)
211 211  (((
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217 217  
218 218  (% class="box warningmessage" %)
219 219  (((
220 -**Note**
221 -\\I find that I receive a "no module named nest" error when trying this right after installing NEST. But it succeeds after a restart. So, if you do observe an error, close all programs, restart your computer, and try again. This time, it should execute as expected.
195 +**Note:**
196 +\\I find that I receive a "no module named nest" error, when trying this right after installing NEST. But it succeeds after a restart. So if you do observe an error, close all programs and restart your computer, and try again. This time it should execute as expected.
222 222  )))
223 223  
224 -If there are no error messages here, and the import is successful, we have completed installing NEST simulator and are able to load it via Python.
199 +If there are no error messages here, and the import is successful, then we have completed installing NEST simulator, and are able to load it via Python.
225 225  
226 -We next move on to the third simulator, NEURON. Similar to Brian2, the installation for NEURON can be easily done via the 'pip' command. Do note that this method of installation does not auto-enable MPI support, which would be required for running simulations in parallel. Do visit the NEURON website if you wish to install on clusters or HPC machines.
201 +We next move on to the third simulator, NEURON. The installation for NEURON used to be more involved previously, but can now be easily completed using the 'pip' command:
227 227  
228 228  (% class="box infomessage" %)
229 229  (((
... ... @@ -231,16 +231,15 @@
231 231  \\(% style="color:#000000" %)pip install neuron
232 232  )))
233 233  
234 -This installs the NEURON simulator on our system. To confirm that we have properly installed NEURON, we can test as follows:
209 +This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
235 235  
236 236  (% class="box infomessage" %)
237 237  (((
238 238  **Screencast** - terminal
239 -\\(% style="color:#000000" %)nrniv
240 -\\quit()
214 +\\(% style="color:#000000" %)nrngui
241 241  )))
242 242  
243 -This will display the NEURON banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEURON v8.0.0 on our system. Next, let's verify that this is indeed accessible via Python.
217 +This will display the NEURON banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEURON v8.0.0 on our system. Let us next verify that this is indeed accessible via Python.
244 244  
245 245  (% class="box infomessage" %)
246 246  (((
... ... @@ -250,9 +250,9 @@
250 250  \\exit()
251 251  )))
252 252  
253 -If there are no error messages here, and the import is successful, we have completed installing NEURON simulator and are able to load it via Python.
227 +If there are no error messages here, and the import is successful, then we have completed installing NEURON simulator, and are able to load it via Python.
254 254  
255 -Now that we have installed all the simulators we intend to use, we move on to installing PyNN itself. Because PyNN is a Python package, we can install it easily using the 'pip' command:
229 +Now that we have installed all the simulators we intend to use, we move on to installing PyNN itself. As PyNN is a Python package, we can install it easily using the 'pip' command:
256 256  
257 257  (% class="box infomessage" %)
258 258  (((
... ... @@ -262,11 +262,11 @@
262 262  
263 263  (% class="box warningmessage" %)
264 264  (((
265 -**Note**
266 -\\Note that PyNN project is spelt with a captial P, small y, and two captital N. The pip command is case-insensitive, so you may write it differently here. But the Python module, as we will see later, is case-sensitive and is spelt starting with a small P. This is in line with general Python convention, whereby package names start with small letters. Thus, while importing PyNN module via Python, it needs to be written as 'pyNN'.
239 +**Note:**
240 +\\Note that PyNN project is spelt with a captial P, small y, and two captital N. The pip command is case-insensitive, so you may write it differently here. But the Python module, as we shall see ahead, is spelt starting with a small P. This is in line with general Python convention, whereby package names start with small alphabets.
267 267  )))
268 268  
269 -To verify that PyNN has been successfully installed on our system and that it is indeed able to communicate with the other simulators that we installed earlier, we can try running:
243 +To verify that PyNN has been successfully installed on our system, and that it is indeed able to communicate with the other simulators that we installed earlier, we can try running:
270 270  
271 271  (% class="box infomessage" %)
272 272  (((
... ... @@ -280,7 +280,7 @@
280 280  (% style="color:#000000" %)sim.end()
281 281  )))
282 282  
283 -This confirms that PyNN has been properly setup and also that it is able to employ Brian 2. To verify that PyNN is also able to communicate with NEST and NEURON simulators, we can do the following:
257 +This confirms that PyNN has been properly setup, and also that is able to employ Brian 2. To verify similary that PyNN is also able to communicate with NEURON and NEST simulators:
284 284  
285 285  (% class="box infomessage" %)
286 286  (((
... ... @@ -302,22 +302,14 @@
302 302  (% style="color:#000000" %)sim.end()
303 303  )))
304 304  
305 -This confirms that all the required software packages have been successfully completed and are functioning as expected.
279 +This confirms that all the required software packages have been successfully completed, and are functioning as expected.
306 306  
307 -As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
308 -
309 -(% class="box infomessage" %)
310 -(((
311 -**Screencast** - terminal
312 -\\(% style="color:#000000" %)pip install matplotlib
313 -)))
314 -
315 315  (% class="box successmessage" %)
316 316  (((
317 317  **Slide** recap of learning objectives
318 318  )))
319 319  
320 -That is the end of this tutorial, in which I've demonstrated how to install PyNN and other required simulators in a Linux system. You are now ready to start modeling! To learn about model development in PyNN, take a look at our next tutorial. Also, we will be releasing a series of tutorials, throughout the rest of 2021 and 2022, to introduce more advanced features of PyNN, so keep an eye on the EBRAINS website.
286 +That is the end of this tutorial, in which I've demonstrated how to install PyNN, and other required simulators, in a Linux system. You are now ready to start modeling! To learn about model development in PyNN, do take a look at our next tutorial. Also, we will be releasing a series of tutorials, throughout the rest of 2021 and 2022, to introduce these more advanced features of PyNN, so keep an eye on the EBRAINS website.
321 321  
322 322  (% class="box successmessage" %)
323 323  (((
... ... @@ -336,7 +336,7 @@
336 336  )))
337 337  
338 338  (% class="wikigeneratedid" %)
339 -PyNN has been developed by many different people, with financial support from several organisations. I'd like to mention in particular the CNRS and the European Commission, through the FACETS, BrainScaleS, and Human Brain Project grants.
305 +PyNN has been developed by many different people, with financial support from several different organisations. I'd like to mention in particular the CNRS and the European Commission, through the FACETS, BrainScaleS and Human Brain Project grants.
340 340  
341 341  (% class="wikigeneratedid" %)
342 -For more information, visit neuralensemble.org/PyNN. If you have questions you can contact us through the PyNN Github project, the NeuralEnsemble forum, EBRAINS support, or the EBRAINS Community.
308 +For more information visit neuralensemble.org/PyNN. If you have questions you can contact us through the PyNN Github project, the NeuralEnsemble forum, EBRAINS support, or the EBRAINS Community.